Mercurial > repos > nml > biohansel

annotate biohansel.xml @ 0:c6e29bb1ab31 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
author nml
date Wed, 15 Aug 2018 10:34:50 -0400
parents
children 1f8eccf9d15d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
1 <tool id="biohansel" name="biohansel" version="2.1.0">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
2 <description>SNP subtyping of genome sequence reads or assemblies</description>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
3 <requirements>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
4 <requirement type="package" version="2.1.0">bio_hansel</requirement>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
5 </requirements>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
6 <command detect_errors="exit_code">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
7 <![CDATA[
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
8
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
9 #import re
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
10
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
11 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
12 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$')
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
13
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
14 #def is_gzipped_fastq($data_input)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
15 ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
16 #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz')
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
17 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
18
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
19 #def get_fastq_ext($data_input)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
20 ## Get file extension for FASTQ data param
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
21 #return '.fastq.gz' if $is_gzipped_fastq($data_input) else '.fastq'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
22 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
23
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
24 #def base_sample_name($name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
25 ## Get the base sample name and append 1/2 depending on if forward/reverse read
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
26 #set $illumina_match = $ILLUMINA_REGEX.match($name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
27 #if $illumina_match
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
28 #return $illumina_match.group(1)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
29 #elif $re.search(r'_R(1|2)', $name):
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
30 #return $re.sub(r'(.+)_R(1|2)([^\.]*)(\..+)', r'\1\3', $name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
31 #elif $re.match(r'.+_\d\.', $name):
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
32 #return $re.sub(r'(.+)_(\d)(\..+)', r'\1', $name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
33 #else
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
34 #return $name
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
35 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
36 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
37
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
38 #def get_paired_fastq_filename($data_input, $name=None, $is_forward=True)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
39 ## Get paired FASTQ filename for a data param with appropriate file extension
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
40 ## with '_1' or '_2' appended if forward or reverse reads, respectively.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
41 #set $name = $name if $name is not None else $data_input.name
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
42 #set $name = $base_sample_name($name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
43 #set $postfix = '1' if $is_forward else '2'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
44 #set $ending = '_{}{}'.format($postfix, $get_fastq_ext($data_input))
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
45 #return '"{}"'.format($name) if $ending in $name else '"{}{}"'.format($name, $ending)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
46 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
47
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
48 ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
49 #if $input.type == 'fasta'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
50 #set $input_files = '"{}"'.format($input.fasta.name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
51 ln -s "$input.fasta" $input_files &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
52 #elif $input.type == 'paired'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
53 #set $forward_filename = $get_paired_fastq_filename($input.forward)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
54 #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
55 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
56 ln -s "$input.forward" $forward_filename &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
57 ln -s "$input.reverse" $reverse_filename &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
58 #elif $input.type == 'single'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
59 #set $input_files = '"{}"'.format($input.single.name)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
60 ln -s "$input.single" $input_files &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
61 #elif $input.type == 'paired_collection'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
62 #set $forward_filename = $get_paired_fastq_filename($input.paired_collection.forward)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
63 #set $reverse_filename = $get_paired_fastq_filename($input.paired_collection.reverse, is_forward=False)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
64 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
65 ln -s "$input.paired_collection.forward" $forward_filename &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
66 ln -s "$input.paired_collection.reverse" $reverse_filename &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
67 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
68
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
69 ## Checking for custom scheme.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
70 #if $type_of_scheme.scheme_type == "custom":
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
71 #if $type_of_scheme.scheme_input.is_of_type('fasta'):
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
72 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
73 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
74 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
75
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
76 #def get_subtype_metadata_filename($data_input)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
77 ## Ensure that the subtype metadata table file has the proper extension - .tab or .csv
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
78 #set $filename = $data_input.name
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
79 #if $data_input.is_of_type('tabular')
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
80 #return '{}.tab'.format($filename)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
81 #elif $data_input.is_of_type('csv')
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
82 #return '{}.csv'.format($filename)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
83 #else
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
84 #return None
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
85 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
86 #end def
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
87
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
88 ## Symlink to subtype metadata table if it is specified
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
89 #if $subtype_metadata
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
90 #set global $subtype_metadata_filename = $get_subtype_metadata_filename($subtype_metadata)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
91 #if $subtype_metadata_filename
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
92 ln -s '$subtype_metadata' '$subtype_metadata_filename' &&
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
93 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
94 #else
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
95 #set global $subtype_metadata_filename = None
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
96 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
97
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
98 #################################
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
99 ## biohansel command starts here:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
100 #################################
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
101 hansel
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
102 -vvv
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
103 -t "\${GALAXY_SLOTS:-1}"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
104 -o results.tab
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
105 -O match_results.tab
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
106 -S tech_results.tab
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
107 $dev_args.use_json
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
108 $input_files
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
109 --scheme
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
110 #if $type_of_scheme.scheme_type == "custom":
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
111 '$type_of_scheme.scheme_input.name'
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
112 #else:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
113 $type_of_scheme.scheme_type
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
114 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
115 #if $subtype_metadata_filename
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
116 --scheme-metadata $subtype_metadata_filename
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
117 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
118 #if $kmer_vals.kmer_min
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
119 --min-kmer-freq $kmer_vals.kmer_min
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
120 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
121 #if $kmer_vals.kmer_max
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
122 --max-kmer-freq $kmer_vals.kmer_max
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
123 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
124 #if $qc_vals.low_cov_depth_freq
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
125 --low-cov-depth-freq $qc_vals.low_cov_depth_freq
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
126 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
127 #if $qc_vals.max_missing_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
128 --max-missing-tiles $qc_vals.max_missing_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
129 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
130 #if $qc_vals.min_ambiguous_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
131 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
132 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
133 #if $qc_vals.max_intermediate_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
134 --max-intermediate-tiles $qc_vals.max_intermediate_tiles
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
135 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
136 #if $qc_vals.low_coverage_warning
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
137 --low-cov-warning $qc_vals.low_coverage_warning
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
138 #end if
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
139 ]]>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
140 </command>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
141 <inputs>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
142 <conditional name="input">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
143 <param name="type" type="select" label="Sequence Data Type">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
144 <option value="fasta">Contigs (FASTA)</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
145 <option value="paired">Paired-end reads (FASTQ)</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
146 <option value="single">Single-end reads (FASTQ)</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
147 <option value="paired_collection">Paired-end reads collection (FASTQ)</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
148 </param>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
149 <when value="fasta">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
150 <param name="fasta"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
151 type="data" format="fasta"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
152 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
153 label="Contigs (FASTA)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
154 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
155 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
156 <when value="paired">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
157 <param name="forward"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
158 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
159 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
160 label="Forward reads (FASTQ)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
161 help="Must have ASCII encoded quality scores"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
162 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
163 <param name="reverse"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
164 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
165 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
166 label="Reverse reads (FASTQ)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
167 help="File format must match the Forward FASTQ file"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
168 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
169 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
170 <when value="single">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
171 <param name="single"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
172 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
173 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
174 label="Single-end reads (FASTQ)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
175 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
176 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
177 <when value="paired_collection">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
178 <param name="paired_collection"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
179 type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,txt"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
180 collection_type="paired"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
181 optional="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
182 label="Paired-end reads collection (FASTQ)"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
183 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
184 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
185 </conditional>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
186 <conditional name="type_of_scheme">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
187 <param name="scheme_type" type="select"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
188 label="SNP Subtyping Scheme"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
189 help="Select the SNP subtyping scheme you wish to subtype with">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
190 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
191 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
192 <option value="custom">Specify your own custom scheme</option>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
193 </param>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
194 <when value="heidelberg"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
195 <when value="enteritidis"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
196 <when value="custom">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
197 <param name="scheme_input"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
198 type="data" format="fasta"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
199 label="Your biohansel SNP Subtyping Scheme"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
200 </when>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
201 </conditional>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
202 <param name="subtype_metadata"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
203 type="data" format="tabular,csv"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
204 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
205 label="Scheme Subtype Metadata Table [Optional]"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
206 help="CSV or tab-delimited format only. Must contain a 'subtype' column."
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
207 />
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
208 <!-- K-mer frequencies. -->
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
209 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
210 <param name="kmer_min" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
211 argument="--min-kmer-freq"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
212 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
213 min="0" value="8"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
214 label="Min k-mer frequency/coverage"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
215 help="default = 8"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
216 <param name="kmer_max" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
217 argument="--max-kmer-freq"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
218 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
219 min="1" value="1000"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
220 label="Max k-mer frequency/coverage"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
221 help="default = 1000"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
222 </section>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
223 <!-- Quality Checking Parameters -->
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
224 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
225 <param name="low_cov_depth_freq" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
226 argument="--low-cov-depth-freq"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
227 value="20" min="0"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
228 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
229 label="QC: Frequency below this coverage are considered low coverage"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
230 help="default = 20"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
231 <param name="min_ambiguous_tiles" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
232 argument="--min-ambiguous-tiles"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
233 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
234 value="3" min="0"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
235 label="QC: Min number of tiles missing for Ambiguous Result"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
236 help="default = 3"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
237 <param name="max_missing_tiles" type="float"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
238 argument="--max-missing-tiles"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
239 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
240 value="0.05" min="0" max="1"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
241 label="QC: Decimal Proportion of max allowed missing tiles" help="default = 0.05, valid values {0.0 - 1.0}"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
242 <param name="max_intermediate_tiles" type="float"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
243 argument="--max-intermediate-tiles"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
244 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
245 value="0.05" min="0" max="1"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
246 label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
247 help="default = 0.05, valid values {0.0 - 1.0}"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
248 <param name="low_coverage_warning" type="integer"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
249 argument="--low-cov-warning"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
250 optional="true"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
251 value="20"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
252 label="QC: Overall tile coverage below this value will trigger a low coverage warning"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
253 help="default = 20"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
254 </section>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
255 <section name="dev_args" title="Developer Options" expanded="False">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
256 <param name="use_json"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
257 type="boolean"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
258 checked="false"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
259 truevalue="--json"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
260 falsevalue=""
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
261 label="Output JSON results"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
262 help="Use this option of you need json representations of analysis' details"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
263 </section>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
264 </inputs>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
265 <outputs>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
266 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
267 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
268 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
269 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
270 <filter>dev_args['use_json']</filter>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
271 </data>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
272 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
273 <filter>dev_args['use_json']</filter>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
274 </data>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
275 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
276 <filter>dev_args['use_json']</filter>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
277 </data>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
278 </outputs>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
279 <tests>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
280 <test>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
281 <conditional name="input">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
282 <param name="type" value="fasta"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
283 <param name="fasta" value="SRR1002850_SMALL.fasta"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
284 </conditional>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
285 <param name="type_of_scheme" value="heidelberg"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
286 <output name="results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
287 value="SRR1002850_SMALL.fasta-results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
288 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
289 compare="sim_size"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
290 delta="1000">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
291 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
292 <output name="match_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
293 value="SRR1002850_SMALL.fasta-match_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
294 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
295 compare="sim_size"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
296 delta="16000">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
297 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
298 <output name="tech_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
299 value="SRR1002850_SMALL.fasta-tech_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
300 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
301 lines_diff="0">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
302 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
303 </test>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
304 <test>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
305 <conditional name="input">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
306 <param name="type" value="paired"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
307 <param name="forward" value="SRR5646583_SMALL_1.fastq"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
308 <param name="reverse" value="SRR5646583_SMALL_2.fastq"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
309 </conditional>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
310 <param name="type_of_scheme" value="heidelberg"/>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
311 <output name="tech_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
312 value="SRR5646583_SMALL-tech_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
313 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
314 lines_diff="0">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
315 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
316 <output name="results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
317 value="SRR5646583_SMALL-results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
318 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
319 compare="sim_size"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
320 delta="1000">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
321 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
322 <output name="match_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
323 value="SRR5646583_SMALL-match_results.tab"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
324 ftype="tabular"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
325 compare="sim_size"
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
326 delta="16000">
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
327 </output>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
328 </test>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
329 </tests>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
330 <help><![CDATA[
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
331 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
332
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
333 **Usage**
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
334
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
335 1) Select the sequence data you wish to subtype (FASTAs or FASTQs)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
336 2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg subtyping scheme, *Salmonella enterica* serovar Enteritidis subtyping scheme, or your own custom `biohansel` compatible subtyping scheme)
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
337 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
338 4) Click ``Execute``
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
339
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
340 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
341
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
342
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
343 **Example analysis results of a single FASTA file**
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
344
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
345 Contents of ``results.tab``:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
346
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
347 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
348 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | qc_status | qc_message |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
349 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
350 | SRR1002850_SMALL | heidelberg | 0.5.0 | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | SRR1002850_SMALL.fasta | PASS | |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
351 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
352
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
353
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
354 Contents of ``match_results.tab``:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
355
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
356 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
357 | tilename | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_tile | sample | file_path | scheme | scheme_version | qc_status | qc_message |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
358 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
359 | 2154958-2.2.2.2.1.4 | GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG | True | NODE_1_length_726282_cov_40.4705_ID_1 | 13732 | 2154958 | 2.2.2.2.1.4 | True | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
360 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
361 | negative2131791-2.2.3.1.3 | GCTGGGCGAAATGATGCAGTTCACCACTTGCTC | True | NODE_1_length_726282_cov_40.4705_ID_1 | 36900 | 2131791 | 2.2.3.1.3 | False | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
362 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
363
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
364 *Next 201 lines omitted.*
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
365
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
366
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
367
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
368 **Example analysis results of a single FASTQ readset**
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
369
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
370
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
371 Contents of ``results.tab``:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
372
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
373 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
374 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | avg_tile_coverage | qc_status | qc_message |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
375 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
376 | SRR5646583_SMALL | heidelberg | 0.5.0 | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] | 42.631 | PASS | |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
377 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
378
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
379 Contents of ``match_results.tab``:
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
380
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
381 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
382 | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
383 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
384 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
385 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
386 | 21097-2.2.1.1.1 | GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT | 42 | 21097 | 2.2.1.1.1 | True | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
387 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
388
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
389 *Next 202 lines omitted.*
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
390
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
391
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
392 **Example Subtype Metadata**
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
393
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
394 A column with name `subtype` must exist and should have subtype designations that would appear in your biohansel results. There are no requirements for the number of columns or contents of those columns in the table - they can contain whatever you want.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
395
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
396
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
397 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
398 | subtype | clade | source | disease_symptoms |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
399 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
400 | 1 | I | geese | death |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
401 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
402 | 1.1 | I | moose | burns |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
403 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
404 | 2.2.1.1.1 | II | mouse | boils |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
405 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
406 | 2.2.2.2.1.4 | IIa | house | rash |
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
407 +-------------+-------+--------+------------------+
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
408
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
409 The `biohansel` results table will be joined with the subtype metadata table on the `subtype` field so if there are subtype metadata for your `biohansel` results, it will show up in the final output table. For example, if you have a sample that produces a result with subtype "1", there will also be columns "clade", "source" and "disease_symptoms" with "I", "geese" and "death", respectively.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
410
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
411
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
412 Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory.
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
413
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
414 ]]></help>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
415 <citations>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
416 <citation type="bibtex">@ARTICLE{a1,
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
417 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America},
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
418 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash},
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
419 url = {https://github.com/phac-nml/bio_hansel}
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
420 }
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
421 }</citation>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
422 </citations>
c6e29bb1ab31 planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
nml
parents:
diff changeset
423 </tool>